MolNFT v1 · #157065 · protein

Anti-HIV-1 Fab 2G12 + MAN8 re-refinement

6MNF · Fab 2G12, light chain: “Anti-HIV-1 Fab 2G12 + MAN8 re-refinement”. X-ray diffraction, 2 ligands (MAN, BMA), 10 pockets (best druggability 0.75). MolNFT v1 #157065 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6MNF
Type: protein
Length: 874 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab 2G12, light chain; Fab 2G12, heavy chain
Ligands: MAN, BMA
Pockets: 10 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, K	Fab 2G12, light chain	protein	213	6% helix, 53% strand	—
H, M	Fab 2G12, heavy chain	protein	224	7% helix, 50% strand	—

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · 7 copies · chains K, M
BMA · beta-D-mannopyranose · sugar · chains M

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	953	0.75	0.78	100	empty
2	377	0.62	0.78	48	empty
3	272	0.55	0.76	38	empty
4	225	0.52	0.76	34	empty
5	134	0.51	0.80	33	empty

Interfaces

6 interfaces between chains.

K–M · 999 Å² buried · 12 hydrogen bonds · protein-protein
H–M · 965 Å² buried · 13 hydrogen bonds · protein-protein
L–H · 963 Å² buried · 11 hydrogen bonds · protein-protein
L–M · 958 Å² buried · 7 hydrogen bonds · protein-protein
H–K · 890 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

6MNF · Anti-HIV-1 Fab 2G12 + Man8 re-refinement · the same entry in another collection · chain L against L, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 6MNF · PDBe 6MNF

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.